Open Source Python Bio-Informatics Software - Page 4

Synthetic Biology Software Suite (SynBioSS) is composed of a wiki for biochemical kinetic constants, a graphical interface for simulating synthetic biological pathways, and a simulator that runs on either a desktop or supercomputer.

A web-based repository of plasmids and biobricks (see http://parts.mit.edu) plus related utility programs that support synthetic biology research. Note: This project is not updated any longer. A completely re-written and much better version of this web server can be found here: http://www.rotmic.org

Microarray Gene Expression Database Group and OMG Gene Expression Standard (MAGE)

mmView is the web based viewer of macromolecular Crystallographic Information File (mmCIF) format. Online ready-to-use version is available at http://ich.vscht.cz/~cechp/mmcif/ or http://ich.vscht.cz/projects/mmview/

pyQPCR is a GUI application written in python that deals with quantitative PCR (QPCR) raw data. Using quantification cycle values extracted from QPCR instruments, it uses a proven and universally applicable model to give finalized quantification resu

converts a SAM file to fasta file. SAM file is a file output from bwa alignment software. It outputs aligned fasta file.

ABC-SysBio implements likelihood free parameter inference and model selection in dynamical systems. It is designed to work with both stochastic and deterministic models written in Systems Biology Markup Language (SBML).

ABE is a small, fast and convenient program for visualizing and modeling experimental bioassay data. The data can be modeled using either polynomials or a more specific four-parameter model based upon the standard, sigmoidal dose-response curve.

ADDA is a software package for finding domains in protein sequences. ADDA has moved to github (https://github.com/AndreasHeger/adda)

ADOMA stands for: Alternative Display Of Multiple Alignment. ADOMA can create four different displays of a multiple sequence alignment: a ClustalW alignment in HTML format, a simplified ClustalW alignment in HTML and/or txt format and a colored ClustalW alignment in HTML format. For examples of these outputfiles check the screenshots. ADOMA uses ClustalW to create the multiple alignment from DNA or protein sequences and displays them slightly different than the normal output of ClustalW. ADOMA is a commandline program that can easily be used in pipelines. For more information check the README.md in the Files section. How to cite ADOMA: Zaal, D. and Nota, B. (2016), ADOMA: A Command Line Tool to Modify ClustalW Multiple Alignment Output. Mol. Inf., 35: 42–44. doi: 10.1002/minf.201500083 http://onlinelibrary.wiley.com/doi/10.1002/minf.201500083/abstract

Aberration Detection in Tumour Exome (ADTEx) is a tool for copy number variation (CNV) detection for whole-exome data from paired tumour/matched normal samples.

IMPORTANT: Since publication of the AMBIENT method in BMC Sys Bio, several updates have been made. If you wish to use the version used in the paper it is v0.6.3, however I recommend using the latest version which works in the same way but with additional options and has stability and performance improvements. Thanks for your interest! AMBIENT (Active Modules for Bipartite Networks) is a Python module that uses simulated annealing to find areas of a metabolic network (modules) that have some consistent characteristic. AMBIENT does not require predefined pathways and gives highly specific predictions of affected areas of metabolism. For example, scores for reactions based on transcriptional data of their annotated encoding genes can be used in the network and modules of coordinated expression changes can be found. This provides an alternative to pathway/gene set enrichment analyses which is simultaneously more flexible and more specific.

This project is A Mitochondrial OxydoReduction Simulation System. It consists of two linked projects: a program for displaying and analysing large biomolecular systems (Floral) and a multi-agent simulator for biomolecular oxydoreduction systems (AMORSS).

This software has moved to http://www.poissonboltzmann.org/.

We introduce ARDEN (Artificial Reference Driven Estimation of false positives in NGS data), a novel benchmark that estimates error rates based on real experimental reads and an additionally generated artificial reference genome. It allows the computation of error rates specifically for a dataset and the construction of a ROC-curve. Thereby, it can be used to optimize parameters for read mappers, to select read mappers for a specific problem or also to filter alignments based on quality estimation.

02-14-2014. Hamming distance calculation has been updated. These are python scripts to analyze antibody libraries sequenced by next generation sequencing methods (454, Ion Torrent, MiSeq) as described in D'Angelo et al MAbs. 2014 Jan 1;6(1):160-72.

Affymetrix GeneChip Operating Software (GCOS) is used to control Affymetrix Microarray scanners and fluidic stations. Using the DCOM API, this project provides programmatic scripting of GCOS using Python.

Amplicon is a Python script for designing PCR primer sets. Amplicon is written in Python 2.3 and Tkinter 8.4. The current script was created for Windows and an executable is available. Future versions of the script should be able to run on Linux and Mac

In Systems Biology models are created in various formats (Matlab, Java, C/C++, Python, ...). "Annotate Your Model" will help you to link your model to biological web resources by creating a CSV file containing MIRIAM annotations.

ArrayOligoSelector (AOS) systematically designs gene specific long oligo probes for entire genomes. The program optimizes the oligo selections for several parameters, including uniqueness in the genome, internal repeats, self-binding, and GC content.

This is the backend source code of the Atlas2-Cloud pipeline on Amazon which starts and terminates worker nodes, runs analysis and monitors worker instances. It is PRIMARILY meant to be used through Amazon Web Services (AWS) management console by looking for the public Atlas2-Cloud machine image. Alternatively, the code can also be used for running the pipeline from your computer. By installing this software on your computer you will be setting up your computer to act as the head node which would then run the pipeline from your computer.

We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. In silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization.

A collection of bioinformatics-related software created by members of Cancer Research UK (possibly among others).

Image analysis program that extract the movements of the bacteria from digitised movies and data processing associated.

BayesRate is a program to estimate speciation and extinction rates from dated phylogenies in a Bayesian framework. The methods are described in: Silvestro, D., Schnitzler, J. and Zizka, G. (2011) A Bayesian framework to estimate diversification rates and their variation through time and space. BMC Evolutionary Biology, 11, 311 Silvestro D., Zizka G. & Schulte K. (2014) Disentangling the effects of key innovations on the diversification of Bromelioideae (Bromeliaceae). Evolution, 68, 163-175.